gen_feat_mat: Generate Feature Matrix.

In metabodecon: Deconvolution and Alignment of 1d NMR Spectra

Generate Feature Matrix.

Description

Helper function of align(). Should not be called directly by the user.

Generates a list of elements required by speaq_align(). See 'Value' for a detailed description of the list elements.

Direct usage of this function has been deprecated with metabodecon version 1.4.3 and will be removed with metabodecon version 2.0.0.

Usage

gen_feat_mat(
  data_path,
  ppm_range = get_ppm_range(data_path),
  si_size_real_spectrum = length(data_path$y_values),
  scale_factor_x = 1000,
  warn = TRUE
)

Arguments

data_path	A list of deconvoluted spectra as returned by generate_lorentz_curves(). In older versions, this could also be the path passed to generate_lorentz_curves(), but this is deprecated and will trigger a warning. See 'Details' for more information.
ppm_range	The ppm range over which your signals are distributed.
si_size_real_spectrum	Number of data points in your spectra.
scale_factor_x	The x scale factor used during the deconvolution.
warn	Whether to print a warning in case a file path is passed to data_path instead of a list of deconvoluted spectra.

Details

Before version 1.2 of metabodecon, the deconvolution functions generate_lorentz_curves and MetaboDecon1D wrote their output partially as txt files to their input folder. Back then, gen_feat_mat() used those txt files as input to generate the feature matrix. Since version 1.2 these txt files are no longer created by default, to prevent accidental modifications of the input folders. Therefore, the recommended way to pass the required information to gen_feat_mat() is to directly pass the output of generate_lorentz_curves() to gen_feat_mat(). However, to stay backwards compatible, the name of parameter data_path was not changed and passing an actual path to data_path is still possible, but will result in a warning (unless warn is set to FALSE).

Value

A list with the following elements:

data_matrix: A data.frame where each row corresponds to one spectrum and each column to one data point, i.e. for 10 input spectra with 131072 data points each data_matrix would have dimensions 10 x 131072.

peakList: A list of vectors, where each vector contains the indices of the peaks in the corresponding spectrum. The indices increase from left to right, i.e. the smallest index corresponds to the highest ppm value, as the ppm values decrease from left to right.

w: A list of vectors where each vector contains the "position parameter" of the peaks in the corresponding spectrum.

A: A list of vectors where each vector contains the "area parameter" of the peaks in the corresponding spectrum.

lambda: A list of vectors where each vector contains the "width parameter" of the peaks in the corresponding spectrum.

Author(s)

2021-2024 Wolfram Gronwald: initial version.
2024-2025 Tobias Schmidt: refactored initial version.

Examples

sim_subset <- metabodecon_file("sim_subset")
decons <- generate_lorentz_curves_sim(sim_subset)
obj <- gen_feat_mat(decons)
str(obj, 2, give.attr = FALSE)

metabodecon documentation built on Nov. 5, 2025, 7:12 p.m.